Recombination and selection shape the molecular diversity pattern of nitrogen‐fixing Sinorhizobium sp. associated to Medicago

Abstract

We investigate the genetic structure and molecular selection pattern of a sympatric population of Sinorhizobium meliloti and Sinorhizobium medicae. These bacteria fix nitrogen in association with plants of the genus Medicago. A set of 116 isolates were obtained from a soil sample, from root nodules of three groups of plants representing among-species, within-species and intraline diversity in the Medicago genus. Bacteria were characterized by sequencing at seven loci evenly distributed along the genome of both Sinorhizobium species, covering the chromosome and the two megaplasmids. We first test whether the diversity of host plants influence the bacterial diversity recovered. Using the same data set, we then analyse the selective pattern at each locus. There was no relationship between the diversity of Medicago plants that were used for sampling and the diversity of their symbionts. However, we found evidence of selection within each of the two main symbiotic regions, located on the two different megaplasmids. Purifying selection or a selective sweep was found to occur in the nod genomic region, which includes genes involved in nodulation specificity, whereas balancing selection was detected in the exo region, close to genes involved in exopolysaccharide production. Such pattern likely reflects the interaction between host plants and bacterial symbionts, with a possible conflict of interest between plants and cheater bacterial genotypes. Recombination appears to occur preferentially within and among loci located on megaplasmids, rather than within the chromosome. Thus, recombination may play an important role in resolving this conflict by allowing different selection patterns at different loci.

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

“…Based on sequencing of several loci, S. medicae is less diverse than S. meliloti, especially at chromosomal loci (Bailly et al, 2006;van Berkum et al, 2006). Indications of directional and balancing selection have been identified for the nod gene region on pSMED02/pSymA and the region involved in polysaccharide synthesis on pSMED01/pSymB, respectively, in sympatric populations of S. meliloti and S. medicae (Bailly et al, 2006). Such diversity patterns suggest that recombination has an important role in shaping the diversity of both species.…”

“…Although S. meliloti 1021 does not have any comparable plasmid, additional plasmids have also been observed in some other strains of this species Olivares, 1993, 1994;Stiens et al, 2006Stiens et al, , 2007Kuhn et al, 2008). Based on sequencing of several loci, S. medicae is less diverse than S. meliloti, especially at chromosomal loci (Bailly et al, 2006;van Berkum et al, 2006). Indications of directional and balancing selection have been identified for the nod gene region on pSMED02/pSymA and the region involved in polysaccharide synthesis on pSMED01/pSymB, respectively, in sympatric populations of S. meliloti and S. medicae (Bailly et al, 2006).…”

“…Such diversity patterns suggest that recombination has an important role in shaping the diversity of both species. Within each species, linkage disequilibrium analyses suggest that homologous recombination occurs preferentially at loci located on the chromid and megaplasmid, rather than the chromosome (Bailly et al, 2006).…”

Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.

“…The ad hoc Committee for the Re-evaluation of the Species Definition in Bacteriology (Stackebrandt et al, 2002;Gevers et al, 2005) suggested the sequence analysis of a set of protein-encoding genes as alternative phylogenetic markers, or multilocus sequence analysis (MLSA). Several recent studies have confirmed that sequences from housekeeping genes can be used for identification at the species level (Wertz et al, 2003;Zeigler, 2003), for evolutionary population genetics and in taxonomy (Stepkowski et al, 2003;Vinuesa et al, 2005a,b;Bailly et al, 2006). The analysis of a small number of carefully selected gene sequences may equal or even surpass the precision of DNA-DNA hybridization for the quantification of genome relatedness and this approach thus has the potential to replace cumbersome DNA-DNA hybridizations (Zeigler, 2003, Martens et al, 2008.…”

“…'Ensifer mexicanus' and 'Sinorhizobium chiapanecum' were described using phenotypic analysis, phylogenies of the recA, gyrA, nolR, rpoB, rrs and symbiotic genes and confidence intervals of sequence similarity to estimate both inter-and intraspecies variation; all were in correlation with DNA-DNA hybridization data (Lloret et al, 2007;Rincó nRosales et al, 2009). In addition, MLSA has been applied in diversity studies of the genera Enterococcus, Aeromonas and Ensifer (Sinorhizobium) (Naser et al, 2005;Soler et al, 2004;Bailly et al, 2006) and it has been reported as being a highly reproducible and economical method for rapid and reliable species identification.…”